Is SLC5A1 p.Asp2= (c.6C>T) pathogenic?

SLC5A1 p.Asp2= (c.6C>T) is classified Benign in SLC5A1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 7.03%, amr) — too common for a highly-penetrant pathogenic allele; Associated with glucose-galactose malabsorption.

What condition is associated with SLC5A1 p.Asp2= (c.6C>T)?

SLC5A1 p.Asp2= (c.6C>T) is associated with glucose-galactose malabsorption (ClinVar).

How is Glucose-galactose malabsorption inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SLC5A1 p.Asp2=

Q: How common is SLC5A1 p.Asp2= (c.6C>T) in the general population?

SLC5A1 p.Asp2= (c.6C>T) is common (popmax 7.03%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.6C>T · rs33973317 · VCV341234

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 7.03%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

glucose-galactose malabsorption

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	phastCons 0.87
Overall
CADD	9.29	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.03% Admixed American · 4,216/60,010 alleles

Filtering AF 6.85% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.78%

Overall 1.14% 18,429/1,614,004 alleles · common exomes 16,647/1,461,648 · genomes 1,782/152,356 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	7.03%	14
Ashkenazi Jewishnot grpmax-eligible	2.87%	35
Amishnot grpmax-eligible	2.08%	48
Remaining individualsnot grpmax-eligible	1.16%	86
European (non-Finnish)	0.993%	101
Middle Eastern	0.545%	184
South Asian	0.468%	214
Finnishnot grpmax-eligible	0.393%	254
African / African-American	0.248%	404
East Asian	0.00446%	22,441

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SLC5A1
Protein: p.Asp2=
Coding: c.6C>T
MANE Select: NM_000343
dbSNP: rs33973317
Type: single nucleotide variant
Location: chr22:32043287 (GRCh38)
Gene constraint: LOEUF 0.705 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 84.53 · 4 PDB

Full SLC5A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glucose-galactose malabsorption — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glucose-galactose malabsorption (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

SLC5A1 p.Arg267Ter Pathogenic ★★ same condition
SLC5A1 p.Arg336His Likely pathogenic ★★ same condition
SLC5A1 p.Arg63Ter Pathogenic ★★ same condition
SLC5A1 p.Asp28Asn Pathogenic/Likely pathogenic ★★ same condition
SLC5A1 p.Cys255Trp Pathogenic ★★ same condition
SLC5A1 p.Gln457Arg Pathogenic/Likely pathogenic ★★ same condition
SLC5A1 p.Ser159Pro Likely pathogenic ★★ same condition
SLC5A1 p.Trp67Ter Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/slc5a1-p-asp2 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown